[Bioperl-l] Getting read position information from an ACE file?

[Dan Bolser]

Dear Perl Monkeys,

I wrote a little demo script for Bio::Assembly::IO here:

http://www.bioperl.org/wiki/Module:Bio::Assembly::IO


I would very much appreciate comments, criticisms and corrections on
that script (please just edit the wiki). For a newbie its always the
same question, am I doing it right?

In particular, I read about the 4 possible coordinates of a read in an
assembly. My script only retrieves two (?) of the possible four. How
should it be adjusted to print all four coordinates for each read?

Additionally, I'm not sure how to distinguish between the trimmed read
vs. the full length read and/or the aligned portion of the read vs.
the full length read.

What I *really* want is the coordinates of the aligned portion of the
read in gapped read and gapped consensus space, along with the quality
trimmed range of the read.

The ACE file in question is produced by the gsMapper program, which is
part of Newbler from Roche (454), so it has some small
'peculiarities', but I don't think they are critical for the task at
hand.


Thanks very much for any hep you can provide on any of the above issues.

Sincerely,
Dan.